Cycles texture paint independently of UV mapping
I think that you can still use two UV mapped textures but one is the perfect version, and the other is a damaged version. Here in my example, the procedural texture is set to generated coordinate and it is used to reveal the purple color by driving the mix factor of the color mix node. You can see I set the arrays to leave some space so the procedural texture effect is apparent. Better to experiment with procedural textures to see what is the best option here, but this is the best option for now until we get some kind of texture modifier that works on top of arrays and allows a separate uv mapping that includes the rest of the generated mesh.